Convert Between IsoformicExperiment and SummarizedExperiment

as_isoformic() builds an IsoformicExperiment from a SummarizedExperiment (for example the output of tximeta), from a tximport list (abundance, counts, length) or from a named list of matrices. as_summarized_experiment() does the reverse at the transcript or gene level, which is convenient for running Bioconductor tools such as DESeq2 or fishpond on the stored assays (a counts assay is placed first, as those tools expect).

Usage

as_isoformic(
  x,
  annot_path,
  col_data = NULL,
  experiment_name = NULL,
  ignore_after_bar = TRUE,
  drop_unannotated = FALSE
)

as_summarized_experiment(self, level = c("transcript", "gene"), ...)

Arguments

x

A SummarizedExperiment, a tximport list or a named list of matrices.

annot_path

Annotation directory or GFF3/GTF file.

col_data

Sample metadata; taken from colData(x) when x is a SummarizedExperiment.

experiment_name

Optional experiment name.

ignore_after_bar

Logical, truncate GENCODE |-separated transcript IDs.

drop_unannotated

Logical, drop transcripts absent from the annotation instead of failing.

self

An IsoformicExperiment.

level

"transcript" (default) or "gene".

...

Passed on to methods.

Value

as_isoformic() returns an IsoformicExperiment; as_summarized_experiment() returns a SummarizedExperiment.

Examples

iso <- example_isoformic()
txi <- list(abundance = assay(iso, "abundance"), counts = assay(iso, "counts"))
annot <- system.file("extdata", "example_experiment", "annotation", package = "isoformic")
iso2 <- as_isoformic(txi, annot_path = annot, col_data = col_data(iso))
iso2
#> <IsoformicExperiment> isoformic_8f3c1587e6
#>   annotation : gencode_v33_example_subset (69 genes, 892 transcripts, 7,032 exons)
#>   samples    : 25 [condition]
#>   transcripts: 499 assayed from 69 genes
#>   assays     : abundance, counts
#>   gene assays: derived from transcript assays on demand
#>   DE results : <none>

if (requireNamespace("SummarizedExperiment", quietly = TRUE)) {
  se <- as_summarized_experiment(iso, level = "gene")
  se
}
#> class: SummarizedExperiment 
#> dim: 69 25 
#> metadata(5): experiment_name annot_path source annotation note
#> assays(2): counts abundance
#> rownames(69): ENSG00000005007.12 ENSG00000005206.17 ...
#>   ENSG00000229807.12 ENSG00000270641.1
#> rowData names(14): gene_id gene_name ... end_pos gene_strand
#> colnames(25): SRR11498039 SRR11498040 ... SRR11498078 SRR11498079
#> colData names(2): sample_id condition